PASS2: A Database of Structure-Based Sequence Alignments of Protein Structural Domain Superfamilies

Protein Structural Domain Dataset

The information about protein structural domains and their boundaries were obtained from SCOP 1.73v release (Andreeva et al., 2008) and their corresponding structural coordinates, which are having ≤40% sequence identity at their superfamily level, were downloaded from ASTRAL compendium (Chandonia et al., 2004). The current structural database was constructed as in the previous PASS2 version (Bhaduri, Pugalenthi, & Sowdhamini, 2004 2004) with some modifications such as the inclusion of assessment of alignments (Figure 1). According to the number of structural entries in each superfamily, in this update, we have categorized them as single member superfamilies (SMS), two member superfamilies (TMS) and multi-member superfamilies (MMS).

Figure 1.

Flowchart for rigorous structure-based sequence alignment of distantly related proteins

The flowchart describes three phases of the algorithm, namely the initial alignment phase, the final alignment phase and the alignment assessment phase. The initial alignment phase includes building the initial alignment of Two member superfamilies by using programs such as MINRMS or ClustalW or MALIGN and multi-member superfamilies by using programs such as STAMP. The final alignment phase includes deriving the final alignment from the initial equivalences of initial alignment by using the JOY and COMPARER package. The alignment assessment phase includes assessment of the final alignment for extent of structural deviations and secondary structural equivalences. Various features were provided and the new features have been marked in pink.